The Dubai-based airline said in an emailed statement that it denies the allegations and plans to defend itself in a court hearing next month.
Emirates said it does not intend to make any further comments because of the ongoing legal proceedings.
The Australian Competition and Consumer Commission alleges Emirates worked with carriers in Singapore, Indonesia, Hong Kong, the United Arab Emirates and India to fix the prices of air freight rates and surcharges between 2002 and 2006.
Australian regulators have leveled similar charges against eight other airlines.
Six, including Qantas Airways and British Airways, have been ordered to pay penalties ranging from $3 million to $20 million Australian dollars ($2.5 million to $16.5 million).